DreINT0019548 @ danRer10
Intron Retention
Gene
ENSDARG00000002771 | SLC4A5 (1 of 2)
Description
solute carrier family 4 (sodium bicarbonate cotransporter), member 5 [Source:HGNC Symbol;Acc:HGNC:18168]
Coordinates
chr5:27476841-27477201:-
Coord C1 exon
chr5:27477047-27477201
Coord A exon
chr5:27476973-27477046
Coord C2 exon
chr5:27476841-27476972
Length
74 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
GCTGCTGTTGTTTCTGTGAGAAG
3' ss Score
-1.16
Exon sequences
Seq C1 exon
CTCTTCAGTGATGTAGCATATAAAGCCAGAGACAGGGAGGACCTGATTGCAGGCATTGACGAGTTCCTGGACGAGGTGATTGTGCTTCCACCTGGAGAGTGGGACCCCAAAATTCGCATAGAGCCCCCCAAAAAAACTCCCTCAGCAGACAAAAG
Seq A exon
GTAAAGCTCATTTCTCTTCTACGTTTTCTTCAGCCTTTATTTATAAGTCTTAATGCTGCTGTTGTTTCTGTGAG
Seq C2 exon
AAGGAAATCTGTATTTTCCCTCAATGAGCTGGGTCAGATGAACGGGACGGCAGGAGGCGGAGGGCCTATTGAAGAGGATGAAGAGATGCCTGTTCCACATGAGCTCGGCGAAGAGTTGGCTTACACAGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002771:ENSDART00000138140:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.190 A=NA C2=0.378
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=PD(13.4=69.2)
A:
NA
C2:
PF0095516=HCO3_cotransp=PU(1.2=13.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCATTGACGAGTTCCTGGAC
R:
TCCTCTTCAATAGGCCCTCCG
Band lengths:
182-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]